The Arabidopsis AtRaptor genes are essential for post-embryonic plant growth.

Anderson GH, Veit B, Hanson MR - BMC Biol. (2005)

Bottom Line:
AtRaptor transcripts accumulate in dividing and expanding cells and tissues.The data implicate the TOR signaling pathway, a major regulator of cell growth in yeast and metazoans, in the maintenance of growth from the shoot apical meristem in plants.These results provide insights into the ways in which TOR/Raptor signaling has been adapted to regulate plant growth and development, and indicate that in plants, as in other eukaryotes, there is some Raptor-independent TOR activity.

Background: Flowering plant development is wholly reliant on growth from meristems, which contain totipotent cells that give rise to all post-embryonic organs in the plant. Plants are uniquely able to alter their development throughout their lifespan through the generation of new organs in response to external signals. To identify genes that regulate meristem-based growth, we considered homologues of Raptor proteins, which regulate cell growth in response to nutrients in yeast and metazoans as part of a signaling complex with the target of rapamycin (TOR) kinase.

Results: We identified AtRaptor1A and AtRaptor1B, two loci predicted to encode Raptor proteins in Arabidopsis. Disruption of AtRaptor1B yields plants with a wide range of developmental defects: roots are thick and grow slowly, leaf initiation and bolting are delayed and the shoot inflorescence shows reduced apical dominance. AtRaptor1A AtRaptor1B double mutants show normal embryonic development but are unable to maintain post-embryonic meristem-driven growth. AtRaptor transcripts accumulate in dividing and expanding cells and tissues.

Conclusion: The data implicate the TOR signaling pathway, a major regulator of cell growth in yeast and metazoans, in the maintenance of growth from the shoot apical meristem in plants. These results provide insights into the ways in which TOR/Raptor signaling has been adapted to regulate plant growth and development, and indicate that in plants, as in other eukaryotes, there is some Raptor-independent TOR activity.

Figure 1: Raptor proteins in eukaryotes are highly conserved. (A) Similarity plot of Raptor homologues from the vascular plants Arabidopsis, Medicago truncatula and Oryza sativa, the fungus S. pombe (Mip1p), and mammals. The X-axis represents residue number; the Y-axis represents percent identity at that residue from 0% (0) to 100% (1). (B) Schematic diagram showing the position of the Raptor N-terminal Conserved / putative Caspase domain (RNC/C) region, HEAT repeats (H), and WD-40 repeats (WDx7) common to all Raptor proteins. (C) Phylogeny of plant, animal and fungal Raptor proteins. Bootstrap values, calculated using both parsimony (left) and maximum likelihood (right) are shown to the left of the clades they describe. The two Arabidopsis Raptor proteins, AtRaptor1A and AtRaptor1B, resolve as a single clade with 100% confidence. The alignment was generated using Megalign (DNAStar), the similarity plot was generated from this alignment using VectorNTI, and bootstrap values were calculated using PAUP*4.0b.

Mentions:
To determine the time of divergence between the two AtRaptor loci, we searched for Raptor homologues in available plant genome data using AtRaptor1A and AtRaptor1B as query sequences. Full-length Raptor loci were discovered in the available rice (Oryza sativa subspecies japonica) and alfalfa (Medicago truncatula) genome sequences. Using AtRaptor1B and partial cDNA sequence (where available) as guides, we determined putative protein sequences from these loci. Alignment of these sequences with AtRaptor1A, AtRaptor1B, mammalian Raptor, the budding yeast Raptor homologue KOG1 and the fission yeast Raptor homologue Mip1p showed that there is a striking degree of conservation among all Raptor homologues (Fig. 1A; for the complete alignment [see additional file 1]). AtRaptor1B and the Saccharomyces cereviseae Raptor homologue KOG1, the most divergent member included in the analysis, show 28% identity throughout their length. All plant Raptor homologues encode the Raptor N-terminal Conserved / Caspase (RNC/C) motif, HEAT repeats and WD40 motifs first identified in fission yeast Mip1 and characteristic of all Raptor proteins [25,26](Fig. 1B). From this alignment we generated a phylogeny of the Raptor homologues (Fig. 1C). The predicted AtRaptor proteins resolve to a single clade with a high degree of confidence, indicating that the duplication of the AtRaptor loci post-dates the divergence of Arabidopsis from Medicago, and that the loci are likely to encode functionally redundant proteins.

Figure 1: Raptor proteins in eukaryotes are highly conserved. (A) Similarity plot of Raptor homologues from the vascular plants Arabidopsis, Medicago truncatula and Oryza sativa, the fungus S. pombe (Mip1p), and mammals. The X-axis represents residue number; the Y-axis represents percent identity at that residue from 0% (0) to 100% (1). (B) Schematic diagram showing the position of the Raptor N-terminal Conserved / putative Caspase domain (RNC/C) region, HEAT repeats (H), and WD-40 repeats (WDx7) common to all Raptor proteins. (C) Phylogeny of plant, animal and fungal Raptor proteins. Bootstrap values, calculated using both parsimony (left) and maximum likelihood (right) are shown to the left of the clades they describe. The two Arabidopsis Raptor proteins, AtRaptor1A and AtRaptor1B, resolve as a single clade with 100% confidence. The alignment was generated using Megalign (DNAStar), the similarity plot was generated from this alignment using VectorNTI, and bootstrap values were calculated using PAUP*4.0b.

Mentions:
To determine the time of divergence between the two AtRaptor loci, we searched for Raptor homologues in available plant genome data using AtRaptor1A and AtRaptor1B as query sequences. Full-length Raptor loci were discovered in the available rice (Oryza sativa subspecies japonica) and alfalfa (Medicago truncatula) genome sequences. Using AtRaptor1B and partial cDNA sequence (where available) as guides, we determined putative protein sequences from these loci. Alignment of these sequences with AtRaptor1A, AtRaptor1B, mammalian Raptor, the budding yeast Raptor homologue KOG1 and the fission yeast Raptor homologue Mip1p showed that there is a striking degree of conservation among all Raptor homologues (Fig. 1A; for the complete alignment [see additional file 1]). AtRaptor1B and the Saccharomyces cereviseae Raptor homologue KOG1, the most divergent member included in the analysis, show 28% identity throughout their length. All plant Raptor homologues encode the Raptor N-terminal Conserved / Caspase (RNC/C) motif, HEAT repeats and WD40 motifs first identified in fission yeast Mip1 and characteristic of all Raptor proteins [25,26](Fig. 1B). From this alignment we generated a phylogeny of the Raptor homologues (Fig. 1C). The predicted AtRaptor proteins resolve to a single clade with a high degree of confidence, indicating that the duplication of the AtRaptor loci post-dates the divergence of Arabidopsis from Medicago, and that the loci are likely to encode functionally redundant proteins.

Bottom Line:
AtRaptor transcripts accumulate in dividing and expanding cells and tissues.The data implicate the TOR signaling pathway, a major regulator of cell growth in yeast and metazoans, in the maintenance of growth from the shoot apical meristem in plants.These results provide insights into the ways in which TOR/Raptor signaling has been adapted to regulate plant growth and development, and indicate that in plants, as in other eukaryotes, there is some Raptor-independent TOR activity.

Background: Flowering plant development is wholly reliant on growth from meristems, which contain totipotent cells that give rise to all post-embryonic organs in the plant. Plants are uniquely able to alter their development throughout their lifespan through the generation of new organs in response to external signals. To identify genes that regulate meristem-based growth, we considered homologues of Raptor proteins, which regulate cell growth in response to nutrients in yeast and metazoans as part of a signaling complex with the target of rapamycin (TOR) kinase.

Results: We identified AtRaptor1A and AtRaptor1B, two loci predicted to encode Raptor proteins in Arabidopsis. Disruption of AtRaptor1B yields plants with a wide range of developmental defects: roots are thick and grow slowly, leaf initiation and bolting are delayed and the shoot inflorescence shows reduced apical dominance. AtRaptor1A AtRaptor1B double mutants show normal embryonic development but are unable to maintain post-embryonic meristem-driven growth. AtRaptor transcripts accumulate in dividing and expanding cells and tissues.

Conclusion: The data implicate the TOR signaling pathway, a major regulator of cell growth in yeast and metazoans, in the maintenance of growth from the shoot apical meristem in plants. These results provide insights into the ways in which TOR/Raptor signaling has been adapted to regulate plant growth and development, and indicate that in plants, as in other eukaryotes, there is some Raptor-independent TOR activity.